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1 glmnet wrappers
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2 ===============
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3
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4 This is a self installing Galaxy tool exposing the glmnet_ R package which has excellent documentation at
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5 glmnet_ Minimal details are provided in this wrapper - please RTM to get the best out of it.
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6
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7 The tool exposes the entire range of penalised maximum likelihood
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8 GLM models ranging from pure lasso (set alpha to 1) to pure ridge-regression (set alpha to 0).
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9
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10 These models can be k-fold internally cross validated to help select an "optimal" predictive or classification
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11 algorithm. Predictive coefficients for each included independent variable are output for each model.
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12
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13 Predictors can be forced into models to adjust for known confounders or explanatory factors.
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14
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15 The glmnet_ implementation of the coordinate descent algorithm is fast and efficient even on relatively large problems
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16 with tens of thousands of predictors and thousands of samples - such as normalised microarray intensities and anthropometry
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17 on a very large sample of obese patients.
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18
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19 The user supplies a tabular file with rows as samples and columns containing observations, then chooses
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20 as many predictors as required. A separate model will be output for each of potentially multiple dependent
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21 variables. Models are reported as the coefficients for terms in an 'optimal' model.
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22 These optimal predictors are selected by repeatedly setting
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23 aside a random subsample, building a model in the remainder and estimating AUC or deviance
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24 using k (default 10) fold internal cross validation. For each of these steps, a random 1/k
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25 of the samples are set aside and used to estiamte performance of an optimal model estimated
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26 from the remaining samples. Plots are provided showing the range of these (eg 10) internal validation
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27 estimates and mean model AUC (binomial) or residual deviance plots at each penalty increment step.
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28
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29 A full range of link functions are available including Gaussian, Poisson, Binomial and
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30 Cox proportional hazard time to failure for censored data in this wrapper.
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31
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32 Note that multinomial and multiresponse gaussian models are NOT yet implemented since I have not yet
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33 had use for them - send code!
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34
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35 .. _glmnet: http://web.stanford.edu/~hastie/glmnet/glmnet_alpha.html
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36
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37 Wrapper author: Ross Lazarus
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38 19 october 2014
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